AMBER Archive (2007)

Subject: Re: AMBER: chiral surfaces

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Sep 05 2007 - 19:21:51 CDT

I can't say for sure about the other Amber force fields,
but we have tested our ff99SB parameter set and find that it needs no
changes
and provides the correct mirror image Ramachandran surface for D amino
acids.

On 9/5/07, Hector A. Baldoni <hbaldoni_at_unsl.edu.ar> wrote:
>
> Dear amber user,
>
> It is well know that D-amino acid have enantiomeric conformational energy
> surfaces respect to its L-isomers. My question is which terms of the
> dihedral parameters of the function
>
> Etors = ( PK / IDIVF ) * ( 1 + cos ( PN * phi - PHASE) )
>
> I would to modify to catch such behavior on the amber force field.
>
> Thank you for help.
>
>
> ---------------------------------
> Dr. Hector A. Baldoni
> Departamento de Quimica
> UNSL - IMASL - CONICET
> Chacabuco 917 (D5700BWS) San Luis
> Argentina
> hbaldoni_at_unsl.edu.ar
> Tel.:+54-(0)2652-423789 ext. 157
> ----------------------------------
> "Lo sé. Pero no lo acepto. Y no estoy resignada." (I know. But i do no
> approve. And i am not resigned) Edna St. Vincent Millay.
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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